Charge Induced Vortex Lattice Instability

It has been predicted that superconducting vortices should be electrically charged and that this effect is particularly enhanced for, high temperature superconductors.\cite{kho95,bla96} Hall effect\cite{hag91} and nuclear magnetic resonance (NMR) experiments\cite{kum01} suggest the existence of vortex charging, but the effects are small and the interpretation controversial. Here we show that the Abrikosov vortex lattice, characteristic of the mixed state of superconductors, will become unstable at sufficiently high magnetic field if there is charge trapped on the vortex core. Our NMR measurements of the magnetic fields generated by vortices in Bi$_{2}$Sr$_{2}$CaCu$_{2}$O$_{8+y}$ single crystals\cite{che07} provide evidence for an electrostatically driven vortex lattice reconstruction with the magnitude of charge on each vortex pancake of $\mathbf{\sim 2}$x$\mathbf{10^{-3} e}$, depending on doping, in line with theoretical estimates.\cite{kho95,kna05}Comment: to appear in Nature Physics; 6 pages, 7 figure

Ferromagnetic Semiconductors: Moving Beyond (Ga,Mn)As

The recent development of MBE techniques for growth of III-V ferromagnetic semiconductors has created materials with exceptional promise in spintronics, i.e. electronics that exploit carrier spin polarization. Among the most carefully studied of these materials is (Ga,Mn)As, in which meticulous optimization of growth techniques has led to reproducible materials properties and ferromagnetic transition temperatures well above 150 K. We review progress in the understanding of this particular material and efforts to address ferromagnetic semiconductors as a class. We then discuss proposals for how these materials might find applications in spintronics. Finally, we propose criteria that can be used to judge the potential utility of newly discovered ferromagnetic semiconductors, and we suggest guidelines that may be helpful in shaping the search for the ideal material.Comment: 37 pages, 4 figure

Anyons in a weakly interacting system

We describe a theoretical proposal for a system whose excitations are anyons with the exchange phase pi/4 and charge -e/2, but, remarkably, can be built by filling a set of single-particle states of essentially noninteracting electrons. The system consists of an artificially structured type-II superconducting film adjacent to a 2D electron gas in the integer quantum Hall regime with unit filling fraction. The proposal rests on the observation that a vacancy in an otherwise periodic vortex lattice in the superconductor creates a bound state in the 2DEG with total charge -e/2. A composite of this fractionally charged hole and the missing flux due to the vacancy behaves as an anyon. The proposed setup allows for manipulation of these anyons and could prove useful in various schemes for fault-tolerant topological quantum computation.Comment: 7 pages with 3 figures. For related work and info visit http://www.physics.ubc.ca/~fran

Composite Fermion Metals from Dyon Black Holes and S-Duality

We propose that string theory in the background of dyon black holes in four-dimensional anti-de Sitter spacetime is holographic dual to conformally invariant composite Dirac fermion metal. By utilizing S-duality map, we show that thermodynamic and transport properties of the black hole match with those of composite fermion metal, exhibiting Fermi liquid-like. Built upon Dirac-Schwinger-Zwanziger quantization condition, we argue that turning on magnetic charges to electric black hole along the orbit of Gamma(2) subgroup of SL(2,Z) is equivalent to attaching even unit of statistical flux quanta to constituent fermions. Being at metallic point, the statistical magnetic flux is interlocked to the background magnetic field. We find supporting evidences for proposed holographic duality from study of internal energy of black hole and probe bulk fermion motion in black hole background. They show good agreement with ground-state energy of composite fermion metal in Thomas-Fermi approximation and cyclotron motion of a constituent or composite fermion excitation near Fermi-point.Comment: 30 pages, v2. 1 figure added, minor typos corrected; v3. revised version to be published in JHE

Genetic diversity and host alternation of the egg parasitoid Oencyrtus pityocampae between the pine processionary moth and caper bug

Research ArticleThe increased use of molecular tools for species identification in recent decades revealed that each of many apparently generalist parasitoids are actually a complex of morphologically similar congeners, most of which have a rather narrow host range. Ooencyrtus pityocampae (OP), an important egg parasitoid of the pine processionary moth (PPM), is considered a generalist parasitoid. OP emerges from PPM eggs after winter hibernation, mainly in spring and early summer, long before the eggs of the next PPM generation occurs. The occurrence of OP in eggs of the variegated caper bug (CB) Stenozygum coloratum in spring and summer suggests that OP populations alternate seasonally between PPM and CB. However, the identity of OP population on CB eggs seemed uncertain; unlike OP-PPM populations, the former displayed apparently high male/female ratios and lack of attraction to the PPM sex pheromone. We studied the molecular identities of the two populations since the morphological identification of the genus Ooencyrtus, and OP in particular, is difficult. Sequencing of COI and ITS2 DNA fragments and AFLP analysis of individuals from both hosts revealed no apparent differences between the OP-PPM and the OP-CB populations for both the Israeli and the Turkish OPs, which therefore supported the possibility of host alternation. Sequencing data extended our knowledge of the genetic structure of OP populations in the Mediterranean area, and revealed clear separation between East and West Mediterranean populations. The overall level of genetic diversity was rather small, with the Israeli population much less diverse than all others; possible explanations for this finding are discussed. The findings support the possibility of utilizing the CB and other hosts for enhancing biological control of the PPMinfo:eu-repo/semantics/publishedVersio

Male circumcision, religion, and infectious diseases: an ecologic analysis of 118 developing countries

BACKGROUND: Both religious practices and male circumcision (MC) have been associated with HIV and other sexually-transmitted infectious diseases. Most studies have been limited in size and have not adequately controlled for religion, so these relationships remain unclear. METHODS: We evaluated relationships between MC prevalence, Muslim and Christian religion, and 7 infectious diseases using country-specific data among 118 developing countries. We used multivariate linear regression to describe associations between MC and cervical cancer incidence, and between MC and HIV prevalence among countries with primarily sexual HIV transmission. RESULTS: Fifty-three, 14, and 51 developing countries had a high (>80%), intermediate (20–80%), and low (<20%) MC prevalence, respectively. In univariate analyses, MC was associated with lower HIV prevalence and lower cervical cancer incidence, but not with HSV-2, syphilis, nor, as expected, with Hepatitis C, tuberculosis, or malaria. In multivariate analysis after stratifying the countries by religious groups, each categorical increase of MC prevalence was associated with a 3.65/100,000 women (95% CI 0.54-6.76, p = 0.02) decrease in annual cervical cancer incidence, and a 1.84-fold (95% CI 1.36-2.48, p < 0.001) decrease in the adult HIV prevalence among sub-Saharan African countries. In separate multivariate analyses among non-sub-Saharan African countries controlling for religion, higher MC prevalence was associated with a 8.94-fold (95% CI 4.30-18.60) decrease in the adult HIV prevalence among countries with primarily heterosexual HIV transmission, but not, as expected, among countries with primarily homosexual or injection drug use HIV transmission (p = 0.35). CONCLUSION: Male circumcision was significantly associated with lower cervical cancer incidence and lower HIV prevalence in sub-Saharan Africa, independent of Muslim and Christian religion. As predicted, male circumcision was also strongly associated with lower HIV prevalence among countries with primarily heterosexual HIV transmission, but not among countries with primarily homosexual or injection drug use HIV transmission. These findings strengthen the reported biological link between MC and some sexually transmitted infectious diseases, including HIV and cervical cancer

Primary peritoneal and ovarian cancers: an epidemiological comparative analysis

We performed case–control analyses using data from the North Carolina Ovarian Cancer Study to determine risk factors that distinguish primary peritoneal cancer (PPC) from epithelial ovarian cancer (EOC). Our risk factor analyses were restricted to invasive serous cancers including 495 EOC cases, 62 PPC cases and 1,086 control women. Logistic regression analyses were used to calculate adjusted odds ratios and 95% confidence intervals for risk factor associations. Although many case–control associations for the invasive serous PPC cases were similar to those of the invasive serous EOC cases, some differences were observed including a twofold increase in risk of invasive serous PPC in women who were ≥35 years at last pregnancy, whereas a decreased risk was observed for invasive serous EOC risk. We could not confirm a previous report of an association between tubal ligation and PPC, a factor consistently associated with a decreased risk of EOC. The difference in the risk factor associations between invasive serous PPC and EOC cancers suggests divergent molecular development of peritoneal and ovarian cancers. A larger study to determine risk factors for invasive serous PPC is warranted

MIMOX: a web tool for phage display based epitope mapping

BACKGROUND: Phage display is widely used in basic research such as the exploration of protein-protein interaction sites and networks, and applied research such as the development of new drugs, vaccines, and diagnostics. It has also become a promising method for epitope mapping. Research on new algorithms that assist and automate phage display based epitope mapping has attracted many groups. Most of the existing tools have not been implemented as an online service until now however, making it less convenient for the community to access, utilize, and evaluate them. RESULTS: We present MIMOX, a free web tool that helps to map the native epitope of an antibody based on one or more user supplied mimotopes and the antigen structure. MIMOX was coded in Perl using modules from the Bioperl project. It has two sections. In the first section, MIMOX provides a simple interface for ClustalW to align a set of mimotopes. It also provides a simple statistical method to derive the consensus sequence and embeds JalView as a Java applet to view and manage the alignment. In the second section, MIMOX can map a single mimotope or a consensus sequence of a set of mimotopes, on to the corresponding antigen structure and search for all of the clusters of residues that could represent the native epitope. NACCESS is used to evaluate the surface accessibility of the candidate clusters; and Jmol is embedded to view them interactively in their 3D context. Initial case studies show that MIMOX can reproduce mappings from existing tools such as FINDMAP and 3DEX, as well as providing novel, rational results. CONCLUSION: A web-based tool called MIMOX has been developed for phage display based epitope mapping. As a publicly available online service in this area, it is convenient for the community to access, utilize, and evaluate, complementing other existing programs. MIMOX is freely available at

A Collaborative Filtering Approach for Protein-Protein Docking Scoring Functions

A protein-protein docking procedure traditionally consists in two successive tasks: a search algorithm generates a large number of candidate conformations mimicking the complex existing in vivo between two proteins, and a scoring function is used to rank them in order to extract a native-like one. We have already shown that using Voronoi constructions and a well chosen set of parameters, an accurate scoring function could be designed and optimized. However to be able to perform large-scale in silico exploration of the interactome, a near-native solution has to be found in the ten best-ranked solutions. This cannot yet be guaranteed by any of the existing scoring functions

Protein binding hot spots and the residue-residue pairing preference: a water exclusion perspective

<p>Abstract</p> <p>Background</p> <p>A protein binding hot spot is a small cluster of residues tightly packed at the center of the interface between two interacting proteins. Though a hot spot constitutes a small fraction of the interface, it is vital to the stability of protein complexes. Recently, there are a series of hypotheses proposed to characterize binding hot spots, including the pioneering O-ring theory, the insightful 'coupling' and 'hot region' principle, and our 'double water exclusion' (DWE) hypothesis. As the perspective changes from the O-ring theory to the DWE hypothesis, we examine the physicochemical properties of the binding hot spots under the new hypothesis and compare with those under the O-ring theory.</p> <p>Results</p> <p>The requirements for a cluster of residues to form a hot spot under the DWE hypothesis can be mathematically satisfied by a biclique subgraph if a vertex is used to represent a residue, an edge to indicate a close distance between two residues, and a bipartite graph to represent a pair of interacting proteins. We term these hot spots as DWE bicliques. We identified DWE bicliques from crystal packing contacts, obligate and non-obligate interactions. Our comparative study revealed that there are abundant <it>unique </it>bicliques to the biological interactions, indicating specific biological binding behaviors in contrast to crystal packing. The two sub-types of biological interactions also have their own signature bicliques. In our analysis on residue compositions and residue pairing preferences in DWE bicliques, the focus was on interaction-preferred residues (ipRs) and interaction-preferred residue pairs (ipRPs). It is observed that hydrophobic residues are heavily involved in the ipRs and ipRPs of the obligate interactions; and that aromatic residues are in favor in the ipRs and ipRPs of the biological interactions, especially in those of the non-obligate interactions. In contrast, the ipRs and ipRPs in crystal packing are dominated by hydrophilic residues, and most of the anti-ipRs of crystal packing are the ipRs of the obligate or non-obligate interactions.</p> <p>Conclusions</p> <p>These ipRs and ipRPs in our DWE bicliques describe a diverse binding features among the three types of interactions. They also highlight the specific binding behaviors of the biological interactions, sharply differing from the artifact interfaces in the crystal packing. It can be noted that DWE bicliques, especially the unique bicliques, can capture deep insights into the binding characteristics of protein interfaces.</p